‘Real-world’ contaminant exposure of sediment-dwelling biota is typically long-term, low-level and to multiple pollutants. However, sediment quality guidelines, designed to protect these organisms, relate only to single contaminants. This study uses radiometrically dated sediment cores from 7 English lakes with varying contamination histories to reconstruct temporal changes in likely risk to biota (herein termed ‘palaeotoxicity’). The Probable Effects Concentration Quotient (PEC-Q) approach was used to combine sediment concentrations from multiple contaminants (trace metals; PCBs; PBDEs) to determine risk allocated to metals and persistent organic pollutants (POPs) separately as well as combined (PEC-Q Mean-All). Urban-influenced lakes were considerably more contaminated, exceeding PEC-Q thresholds of 0.5 and 2.0 over long durations (some since the nineteenth century). This has been mainly due to metals (principally lead) and by factors of up to 10 for individual metals and by > 2 for PEC-Q Mean-Metals. In 6 out of 7 lakes, considerable reductions in risk associated with trace metals are observed since emissions reductions in the 1970s. However, at all lakes, PEC-Q Mean-POPs has increased sharply since the 1950s and at 5 out of 7 lakes now exceeds PEC-Q Mean-Metals. These organic pollutants are therefore now the dominant driver behind elevated contaminant risk to sediment-dwelling biota and recent temporal trends in PEC-Q Mean-All remain above threshold values as a result. Finally, PEC-Q Mean-All values were compared to standard biological toxicity tests for surface sediments at each site. While chironomid growth and daphniid reproduction were significantly reduced compared to controls at 5 out of 7, and all lakes, respectively, the scale of these reductions showed only limited quantitative agreement with predicted risk.Electronic supplementary materialThe online version of this article (10.1007/s10653-018-0080-5) contains supplementary material, which is available to authorized users.